Variant report

Variant	rs522320
Chromosome Location	chr1:70609129-70609130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr1:70608840-70609384	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:70609121-70609173	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr1:70608735-70609150	IMR90	lung:	n/a	chr1:70608930-70608951
4	SMC3	chr1:70608639-70609411	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr1:70608586-70609303	SK-N-SH	brain:	n/a	chr1:70608930-70608951
6	RAD21	chr1:70608829-70609151	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr1:70608738-70609137	IMR90	lung:	n/a	n/a
8	RAD21	chr1:70608624-70609288	SK-N-SH	brain:	n/a	n/a
9	RAD21	chr1:70608731-70609136	SK-N-SH_RA	brain:	n/a	n/a
10	E2F4	chr1:70608770-70609221	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70591297..70593707-chr1:70608586..70610156,2	K562	blood:
2	chr1:70608921..70611354-chr1:70613745..70615584,2	K562	blood:
3	chr1:70607998..70610574-chr1:70685135..70686722,2	K562	blood:
4	chr1:70606579..70609498-chr1:70685222..70687844,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC7-1	chr1:70607065-70610047	ENSG00000261223.1

No data

Variant related genes	Relation type
LRRC7	TF binding region
ENSG00000116754	Chromatin interaction
ENSG00000228988	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1412867	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17131236	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17131238	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17131241	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274913	0.80[CHD][hapmap]
rs34121744	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35522955	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753818	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs476591	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs549843	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56299138	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56873377	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57098486	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs587567	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60409157	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60598073	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610953	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61785267	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61785269	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61785270	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61785272	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs632047	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs651717	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666163	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664084	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6664480	0.90[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6666941	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6700543	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs676753	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74085998	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7533067	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531879	chr1:70386455-70644617	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005397	chr1:70598803-70634585	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	esv1796744	chr1:70604106-70621290	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv871339	chr1:70605735-70634463	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs522320	WLS	cis	cerebellum	SCAN
rs522320	CTH	cis	lymphoblastoid	seeQTL
rs522320	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70596800-70609200	Weak transcription	Liver	Liver
2	chr1:70599000-70609600	Weak transcription	GM12878-XiMat	blood
3	chr1:70601000-70615400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:70601000-70643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:70601200-70652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:70603000-70614800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:70603400-70648800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:70605200-70612200	Weak transcription	Primary B cells from cord blood	blood
9	chr1:70605400-70639400	Weak transcription	Brain Anterior Caudate	brain
10	chr1:70605800-70609200	Enhancers	NHDF-Ad	bronchial
11	chr1:70605800-70609200	Enhancers	NHLF	lung
12	chr1:70605800-70609600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:70606200-70610600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:70606400-70609800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:70606400-70611200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:70606400-70612200	Weak transcription	Primary T cells from cord blood	blood
17	chr1:70606600-70609200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:70606600-70610200	Weak transcription	NH-A	brain
19	chr1:70606600-70611400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:70606600-70611800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:70606600-70612800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:70606600-70614800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:70606600-70617600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:70606600-70619600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:70606600-70629600	Weak transcription	Fetal Intestine Small	intestine
26	chr1:70606600-70633800	Weak transcription	Fetal Intestine Large	intestine
27	chr1:70606800-70609200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:70606800-70609200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:70606800-70609400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:70606800-70610400	Weak transcription	Fetal Heart	heart
31	chr1:70606800-70612800	Weak transcription	Fetal Kidney	kidney
32	chr1:70606800-70617000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr1:70606800-70627800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:70606800-70634800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:70606800-70634800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:70606800-70651600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:70606800-70661800	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:70607000-70609200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:70607000-70609400	Enhancers	Fetal Brain Male	brain
40	chr1:70607000-70609600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:70607000-70609600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:70607000-70610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:70607000-70611400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:70607000-70611800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:70607000-70611800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:70607000-70612200	Weak transcription	HSMM	muscle
47	chr1:70607000-70612800	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:70607000-70612800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:70607000-70613200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:70607000-70613400	Weak transcription	Ovary	ovary

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